conkit.core.mappings module

Mappings required for the core functionality

class AminoAcidMapping[source]

Bases: enum.Enum

Amino acid mapping to encode an alignment

A = 1
C = 2
D = 3
E = 4
F = 5
G = 6
H = 7
I = 8
K = 9
L = 10
M = 11
N = 12
P = 13
Q = 14
R = 15
S = 16
T = 17
V = 18
W = 19
X = 21
Y = 20
class AminoAcidOneToThree[source]

Bases: enum.Enum

Amino acid mapping to convert one-letter codes to three-letter codes

A = 'ALA'
B = 'ASX'
C = 'CYS'
D = 'ASP'
E = 'GLU'
F = 'PHE'
G = 'GLY'
H = 'HIS'
I = 'ILE'
J = 'XLE'
K = 'LYS'
L = 'LEU'
M = 'MET'
N = 'ASN'
O = 'PYL'
P = 'PRO'
Q = 'GLN'
R = 'ARG'
S = 'SER'
T = 'THR'
U = 'SEC'
V = 'VAL'
W = 'TRP'
X = 'XAA'
Y = 'TYR'
Z = 'GLX'
class AminoAcidThreeToOne[source]

Bases: enum.Enum

Amino acid mapping to convert three-letter codes to one-letter codes

ALA = 'A'
ARG = 'R'
ASN = 'N'
ASP = 'D'
ASX = 'B'
CME = 'C'
CYS = 'C'
GLN = 'Q'
GLU = 'E'
GLX = 'Z'
GLY = 'G'
HIS = 'H'
ILE = 'I'
LEU = 'L'
LYS = 'K'
MET = 'M'
MSE = 'M'
PHE = 'F'
PRO = 'P'
PYL = 'O'
SEC = 'U'
SER = 'S'
THR = 'T'
TRP = 'W'
TYR = 'Y'
UNK = 'X'
VAL = 'V'
XAA = 'X'
XLE = 'J'
class ContactMatchState[source]

Bases: enum.Enum

Enumerated class to store state constants for each contact

false_negative = 4
false_positive = 3
true_negative = 2
true_positive = 1
unknown = 0
class SequenceAlignmentState[source]

Bases: enum.Enum

Alignment states

aligned = 2
unaligned = 1
unknown = 0